As of this posting, FamilySearch, has the following Seamen’s Protection Certificates available online:
Ancestry.com also has the following databases of these documents–FamilySearch does not have them all online and they have not yet been indexed.
- U.S., Seamen’s Protection Certificates, 1792-1869
- Indexes to Seamen’s Protection Certificate Applications and Proofs of Citizenship
- Register of Seamen’s Protection Certificates from the Providence, Rhode Island Customs District, 1796-1870
The National Archives also has a PDF file from 2014 with information on these records as well: